Srinivas Aluru

Srinivas Aluru

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Srinivas Aluru

Srinivas Aluru

Publications by authors named "Srinivas Aluru"

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38Publications

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An SVM-based method for assessment of transcription factor-DNA complex models.

BMC Bioinformatics 2018 Dec 21;19(Suppl 20):506. Epub 2018 Dec 21.

Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, 28223, USA.

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http://dx.doi.org/10.1186/s12859-018-2538-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302363PMC
December 2018

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.

Nat Commun 2018 11 30;9(1):5114. Epub 2018 Nov 30.

School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.

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http://dx.doi.org/10.1038/s41467-018-07641-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6269478PMC
November 2018

A fast adaptive algorithm for computing whole-genome homology maps.

Bioinformatics 2018 09;34(17):i748-i756

School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA.

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https://academic.oup.com/bioinformatics/article/34/17/i748/5
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http://dx.doi.org/10.1093/bioinformatics/bty597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129286PMC
September 2018

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.

J Comput Biol 2018 07 30;25(7):766-779. Epub 2018 Apr 30.

2 National Human Genome Research Institute, National Institutes of Health , Bethesda, Maryland.

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http://dx.doi.org/10.1089/cmb.2018.0036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6067103PMC
July 2018

Fast de Bruijn Graph Compaction in Distributed Memory Environments.

IEEE/ACM Trans Comput Biol Bioinform 2018 Jul 31. Epub 2018 Jul 31.

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http://dx.doi.org/10.1109/TCBB.2018.2858797DOI Listing
July 2018

Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.

IEEE/ACM Trans Comput Biol Bioinform 2019 Jul-Aug;16(4):1117-1131. Epub 2017 Oct 9.

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http://dx.doi.org/10.1109/TCBB.2017.2760829DOI Listing
October 2017

A greedy alignment-free distance estimator for phylogenetic inference.

BMC Bioinformatics 2017 Jun 7;18(Suppl 8):238. Epub 2017 Jun 7.

Institute for Data Engineering and Science, Georgia Institute of Technology, Atlanta, 30332, GA, USA.

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http://dx.doi.org/10.1186/s12859-017-1658-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471951PMC
June 2017

Efficient detection of viral transmissions with Next-Generation Sequencing data.

BMC Genomics 2017 05 24;18(Suppl 4):372. Epub 2017 May 24.

Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA.

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http://dx.doi.org/10.1186/s12864-017-3732-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5461558PMC
May 2017

Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

IEEE/ACM Trans Comput Biol Bioinform 2016 Jan-Feb;13(1):99-111

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http://dx.doi.org/10.1109/TCBB.2015.2430313DOI Listing
December 2016

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.

Microarrays (Basel) 2016 Sep 19;5(3). Epub 2016 Sep 19.

School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5040970PMC
http://dx.doi.org/10.3390/microarrays5030023DOI Listing
September 2016

In search of perfect reads.

BMC Bioinformatics 2015 7;16 Suppl 17:S7. Epub 2015 Dec 7.

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http://dx.doi.org/10.1186/1471-2105-16-S17-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674851PMC
August 2016

SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.

BMC Syst Biol 2016 08 1;10 Suppl 2:47. Epub 2016 Aug 1.

Institute of Computer Science, Johannes Gutenberg University Mainz, Mainz, 55128, Germany.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918
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http://dx.doi.org/10.1186/s12918-016-0300-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977481PMC
August 2016

Guest Editors’ Introduction: Selected Papers from ACM-BCB 2013.

IEEE/ACM Trans Comput Biol Bioinform 2015 Jan-Feb;12(1):2-3

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June 2016

A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem.

J Comput Biol 2016 06 8;23(6):472-82. Epub 2016 Apr 8.

College of Computing, Georgia Institute of Technology , Atlanta, Georgia .

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http://dx.doi.org/10.1089/cmb.2015.0235DOI Listing
June 2016

ALFRED: A Practical Method for Alignment-Free Distance Computation.

J Comput Biol 2016 06 3;23(6):452-60. Epub 2016 May 3.

1 College of Computing, Georgia Institute of Technology , Atlanta, Georgia .

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http://dx.doi.org/10.1089/cmb.2015.0217DOI Listing
June 2016

Large-scale metagenomic sequence clustering on map-reduce clusters.

J Bioinform Comput Biol 2013 Feb 25;11(1):1340001. Epub 2012 Dec 25.

Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1142/S0219720013400015DOI Listing
February 2013

A survey of error-correction methods for next-generation sequencing.

Brief Bioinform 2013 Jan 6;14(1):56-66. Epub 2012 Apr 6.

The Broad institute, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bib/bbs015DOI Listing
January 2013

Reverse engineering and analysis of large genome-scale gene networks.

Nucleic Acids Res 2013 Jan 4;41(1):e24. Epub 2012 Oct 4.

Department of Genetics, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1093/nar/gks904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3592423PMC
January 2013

A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana.

Plant J 2011 Feb 10;65(4):634-46. Epub 2011 Jan 10.

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2010.04449.xDOI Listing
February 2011

Repeat-aware modeling and correction of short read errors.

BMC Bioinformatics 2011 Feb 15;12 Suppl 1:S52. Epub 2011 Feb 15.

Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011, USA.

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http://dx.doi.org/10.1186/1471-2105-12-S1-S52DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044310PMC
February 2011

Reptile: representative tiling for short read error correction.

Bioinformatics 2010 Oct 16;26(20):2526-33. Epub 2010 Aug 16.

Department of Electrical and Computer Engineering, Iowa State University, Ames IA 50011, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq468DOI Listing
October 2010

The B73 maize genome: complexity, diversity, and dynamics.

Authors:
Patrick S Schnable Doreen Ware Robert S Fulton Joshua C Stein Fusheng Wei Shiran Pasternak Chengzhi Liang Jianwei Zhang Lucinda Fulton Tina A Graves Patrick Minx Amy Denise Reily Laura Courtney Scott S Kruchowski Chad Tomlinson Cindy Strong Kim Delehaunty Catrina Fronick Bill Courtney Susan M Rock Eddie Belter Feiyu Du Kyung Kim Rachel M Abbott Marc Cotton Andy Levy Pamela Marchetto Kerri Ochoa Stephanie M Jackson Barbara Gillam Weizu Chen Le Yan Jamey Higginbotham Marco Cardenas Jason Waligorski Elizabeth Applebaum Lindsey Phelps Jason Falcone Krishna Kanchi Thynn Thane Adam Scimone Nay Thane Jessica Henke Tom Wang Jessica Ruppert Neha Shah Kelsi Rotter Jennifer Hodges Elizabeth Ingenthron Matt Cordes Sara Kohlberg Jennifer Sgro Brandon Delgado Kelly Mead Asif Chinwalla Shawn Leonard Kevin Crouse Kristi Collura Dave Kudrna Jennifer Currie Ruifeng He Angelina Angelova Shanmugam Rajasekar Teri Mueller Rene Lomeli Gabriel Scara Ara Ko Krista Delaney Marina Wissotski Georgina Lopez David Campos Michele Braidotti Elizabeth Ashley Wolfgang Golser HyeRan Kim Seunghee Lee Jinke Lin Zeljko Dujmic Woojin Kim Jayson Talag Andrea Zuccolo Chuanzhu Fan Aswathy Sebastian Melissa Kramer Lori Spiegel Lidia Nascimento Theresa Zutavern Beth Miller Claude Ambroise Stephanie Muller Will Spooner Apurva Narechania Liya Ren Sharon Wei Sunita Kumari Ben Faga Michael J Levy Linda McMahan Peter Van Buren Matthew W Vaughn Kai Ying Cheng-Ting Yeh Scott J Emrich Yi Jia Ananth Kalyanaraman An-Ping Hsia W Brad Barbazuk Regina S Baucom Thomas P Brutnell Nicholas C Carpita Cristian Chaparro Jer-Ming Chia Jean-Marc Deragon James C Estill Yan Fu Jeffrey A Jeddeloh Yujun Han Hyeran Lee Pinghua Li Damon R Lisch Sanzhen Liu Zhijie Liu Dawn Holligan Nagel Maureen C McCann Phillip SanMiguel Alan M Myers Dan Nettleton John Nguyen Bryan W Penning Lalit Ponnala Kevin L Schneider David C Schwartz Anupma Sharma Carol Soderlund Nathan M Springer Qi Sun Hao Wang Michael Waterman Richard Westerman Thomas K Wolfgruber Lixing Yang Yeisoo Yu Lifang Zhang Shiguo Zhou Qihui Zhu Jeffrey L Bennetzen R Kelly Dawe Jiming Jiang Ning Jiang Gernot G Presting Susan R Wessler Srinivas Aluru Robert A Martienssen Sandra W Clifton W Richard McCombie Rod A Wing Richard K Wilson

Science 2009 Nov;326(5956):1112-5

Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.

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http://www.dawelab.org/wp-content/uploads/2011/03/schnable-2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1178534
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http://dx.doi.org/10.1126/science.1178534DOI Listing
November 2009

Parallel short sequence assembly of transcriptomes.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S14. Epub 2009 Jan 30.

Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648799PMC
January 2009

Guest Editors' Introduction, Special Issue on High-Performance Computational Biology.

Parallel Comput 2008 Nov;34(11):613-615

College of Computing, Georgia Institute of Technology, Atlanta, GA 30332.

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http://dx.doi.org/10.1016/j.parco.2008.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621331PMC
November 2008

Consensus genetic maps as median orders from inconsistent sources.

IEEE/ACM Trans Comput Biol Bioinform 2008 Apr-Jun;5(2):161-71

Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50014, USA.

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http://dx.doi.org/10.1109/TCBB.2007.70221DOI Listing
July 2008

Consensus genetic maps: a graph theoretic approach.

Proc IEEE Comput Syst Bioinform Conf 2005 :35-43

Dept. of Electrical and Computer Engineering, Iowa State University, Ames, IA 50010, USA.

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May 2007

Efficient algorithms and software for detection of full-length LTR retrotransposons.

Proc IEEE Comput Syst Bioinform Conf 2005 :56-64

Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA.

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May 2007

Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution.

Genetics 2007 Jan 16;175(1):429-39. Epub 2006 Nov 16.

Interdepartmental Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, Iowa 50011, USA.

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http://dx.doi.org/10.1534/genetics.106.064006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1774996PMC
January 2007

Space-conserving optimal DNA-protein alignment.

Proc IEEE Comput Syst Bioinform Conf 2004 :80-8

Department of Electrical and Computer Engineering, Iowa State University, USA.

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July 2006

Efficient algorithms and software for detection of full-length LTR retrotransposons.

J Bioinform Comput Biol 2006 Apr;4(2):197-216

Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011, USA.

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April 2006

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes.

Proc Natl Acad Sci U S A 2005 Aug 15;102(34):12282-7. Epub 2005 Aug 15.

Interdepartmental Genetics Graduate Program, L. H. Baker Center for Bioinformatics and Biological Statistics, Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1073/pnas.0503394102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1186025PMC
August 2005

A strategy for assembling the maize (Zea mays L.) genome.

Bioinformatics 2004 Jan;20(2):140-7

Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth017DOI Listing
January 2004

PCAP: a whole-genome assembly program.

Genome Res 2003 Sep;13(9):2164-70

Department of Computer Science Iowa State University, Ames, Iowa 50011-1040, USA.

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http://dx.doi.org/10.1101/gr.1390403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403719PMC
September 2003

Efficient clustering of large EST data sets on parallel computers.

Nucleic Acids Res 2003 Jun;31(11):2963-74

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC156714PMC
http://dx.doi.org/10.1093/nar/gkg379DOI Listing
June 2003